rs2357322 and rs17726078 Contribute to Breast Cancer Risk by Regulating DLX2 Expression

Breast cancer is the most abundant cancer type in female. Genome-wide association study suggests that rs2016394, one SNP at the intron of DLX2 divergent transcript (DLX2-DT), is significantly associated with this disease. Through 1000 genomes project data analysis, it is observed that another three SNPs, rs743605, rs2357322, and rs17726078, show strong linkage disequilibrium with rs2016394. However, the functional SNP(s) and mechanism are still unknown.

Functional genomics effort was performed for this locus.

Through luciferase assay, it is disclosed that rs743605 and rs2016394 are not with the ability to alter gene expression. In contrast, rs2357322 and rs17726078 alleles present significantly different luciferase expression, thus suggesting that these two SNPs are functional mutations. Chromosome conformation capture indicates that DLX2 (distal-less Homeobox 2) can interact with the cis-regulatory element containing these two SNPs and should be the regulatory target. Chromatin immunoprecipitation suggests that transcription factor MYC (MYC proto-oncogene, bHLH transcription factor) can bind the rs17726078 surrounding region. Knock-out of the segment containing these two SNPs by CRISPR/Cas9 can significantly increase DLX2 mRNA and protein expression, cell proliferation, colony formation, migration, and wound healing, thus suggesting that the cis-regulatory element is an attenuator for gene expression.

rs2357322 and rs17726078 might influence DLX2 expression and further contribute to breast cancer risk.